| We developed a protein communication system to capture the genetic information storage and transmission apparatus, where the transmitted messages are protein sequences and the encoded messages are the corresponding DNA. A series connection of the protein communication channel is equivalent to a channel through time: the channel of evolution. We studied the evolutionary dynamics of the protein communication channel in both cases of constant and time-varying point mutation rate. We found that messages sent through the channel of evolution are received according to a fixed probability distribution, which is independent of the original message. Investigation of the information theoretic bounds of the channel of evolution provided tremendous insight into the dynamics of the evolutionary processes of the three branches of life.; We then investigated the structure of the genetic codeword, the DNA. We proved that the introns play the role of a decoy in absorbing mutations in the same way hollow uninhabited structures are used by the military to protect important installations. Our approach is based on a probability of error analysis, where errors are mutations which occur in the exon sequences. Given that introns also drive biological evolution by increasing the rate of unequal crossover between genes, we concluded that the role of introns is to maintain a fine balance between stability and adaptability in eukaryotic genomes.; Finally, we brought to bear new non-stationary methods to shed new light and help resolve the issues of (i) the existence of long-range correlations in DNA sequences and (ii) whether they are present in both coding and non-coding segments or only in the latter. It turns out that the statistical differences between coding and non-coding segments are much more subtle than previously thought using stationary analysis. In particular, both coding and non-coding sequences exhibit long-range correlations as attested by a time-dependent 1/f spectrum. However, we introduced an index of randomness to demonstrate that coding sequences, although not random as previously suspected, are often "more random" (i.e., whiter) than non-coding sequences. Moreover, the study of the evolution of the rate of change of the time-dependent spectral exponent in homologous gene families shows a sudden jump around the rat, which might be related to the well-known supercharged evolution of this rodent. |
